ACLAB

General Information

Remote File Access

From the Cornell campus network, users can access aclab file systems remotely from their computers:

  • Home Directories: users can access home directories at smb://aclab.cac.cornell.edu (Linux or macOS) or \aclab.cac.cornell.edu (Windows)
  • /home/shared/aclab-fmri: users can access this directory at smb://aclab.cac.cornell.edu/aclab-fmri (Linux or macOS) or \aclab.cac.cornell.edu\aclab-fmri (Windows)

Software

Work with Environment Modules

Set up the working environment for each package using the module command. The module command will activate dependent modules if there are any. To show currently loaded modules: (These modules are loaded by default system configurations)

-bash-4.2$ module list

Currently Loaded Modules:
    1) autotools   3) gnu9/9.3.0   5) libfabric/1.10.1   7) ohpc
    2) prun/2.0    4) ucx/1.8.0    6) openmpi4/4.0.4

To show all available modules:

-bash-4.2$ module avail

-------------------- /opt/ohpc/pub/moduledeps/gnu9-openmpi4 --------------------
adios/1.13.1        netcdf-fortran/4.5.2    py3-mpi4py/3.0.3
boost/1.73.0        netcdf/4.7.3            py3-scipy/1.5.1
fftw/3.3.8          opencoarrays/2.8.0      scalapack/2.1.0
hypre/2.18.1        petsc/3.13.1            slepc/3.13.2
mfem/4.1            phdf5/1.10.6            superlu_dist/6.1.1
mumps/5.2.1         pnetcdf/1.12.1          trilinos/13.0.0
netcdf-cxx/4.3.1    ptscotch/6.0.6

------------------------ /opt/ohpc/pub/moduledeps/gnu9 -------------------------
gsl/2.6        mpich/3.3.2-ofi    openmpi4/4.0.4   (L)
hdf5/1.10.6    mvapich2/2.3.2     py3-numpy/1.19.0
metis/5.1.0    openblas/0.3.7     superlu/5.2.1

-------------------------- /opt/ohpc/pub/modulefiles ---------------------------
autotools    (L)    libfabric/1.10.1 (L)    pmix/3.1.4
cmake/3.16.2        ohpc             (L)    prun/2.0   (L)
gnu9/9.3.0   (L)    os                      ucx/1.8.0  (L)

Where:
 L:  Module is loaded

 Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".

To load a module and verify:

-bash-4.2$ module load cmake
-bash-4.2$ module list

Currently Loaded Modules:
    1) autotools   3) gnu9/9.3.0   5) libfabric/1.10.1   7) ohpc
    2) prun/2.0    4) ucx/1.8.0    6) openmpi4/4.0.4     8) cmake/3.16.2

Manage Modules in Your Python Virtual Environment

python 3.6.8 is installed. Users can manage their own python environment (including installing needed modules) using virtual environments. Please see the documentation on virtual environments on python.org for details.

Create Virtual Environment

You can create as many virtual environments, each in their own directory, as needed.

python3 -m venv <your virtual environment directory>

Activate Virtual Environment

You need to activate a virtual environment before using it:

source <your virtual environment directory>/bin/activate

Install Python Modules Using pip

After activating your virtual environment, you can now install python modules for the activated environment:

  • It's always a good idea to update pip first:

    pip install --upgrade pip
    
  • Install the module

    pip install <module name>
    
  • List installed python modules in the environment:

    pip list modules
    
  • Examples: Install tensorflow and keras like this:

    -bash-4.2$ python3 -m venv tensorflow
    -bash-4.2$ source tensorflow/bin/activate
    (tensorflow) -bash-4.2$ pip install --upgrade pip
    Collecting pip
        Using cached https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl
    Installing collected packages: pip
        Found existing installation: pip 18.1
            Uninstalling pip-18.1:
                Successfully uninstalled pip-18.1
    Successfully installed pip-19.2.3
    (tensorflow) -bash-4.2$ pip install tensorflow keras
    Collecting tensorflow
        Using cached https://files.pythonhosted.org/packages/de/f0/96fb2e0412ae9692dbf400e5b04432885f677ad6241c088ccc5fe7724d69/tensorflow-1.14.0-cp36-cp36m-manylinux1_x86_64.whl
    :
    :
    :
    Successfully installed absl-py-0.8.0 astor-0.8.0 gast-0.2.2 google-pasta-0.1.7 grpcio-1.23.0 h5py-2.9.0 keras-2.2.5 keras-applications-1.0.8 keras-preprocessing-1.1.0 markdown-3.1.1 numpy-1.17.1 protobuf-3.9.1 pyyaml-5.1.2 scipy-1.3.1 six-1.12.0 tensorboard-1.14.0 tensorflow-1.14.0 tensorflow-estimator-1.14.0 termcolor-1.1.0 werkzeug-0.15.5 wheel-0.33.6 wrapt-1.11.2
    (tensorflow) -bash-4.2$ pip list modules
    Package              Version
    -------------------- -------
    absl-py              0.8.0  
    astor                0.8.0  
    gast                 0.2.2  
    google-pasta         0.1.7  
    grpcio               1.23.0 
    h5py                 2.9.0  
    Keras                2.2.5  
    Keras-Applications   1.0.8  
    Keras-Preprocessing  1.1.0  
    Markdown             3.1.1  
    numpy                1.17.1 
    pip                  19.2.3 
    protobuf             3.9.1  
    PyYAML               5.1.2  
    scipy                1.3.1  
    setuptools           40.6.2 
    six                  1.12.0 
    tensorboard          1.14.0 
    tensorflow           1.14.0 
    tensorflow-estimator 1.14.0 
    termcolor            1.1.0  
    Werkzeug             0.15.5 
    wheel                0.33.6 
    wrapt                1.11.2
    

Software List

Software Path Notes
*GNU Compilers 9.3.0 /opt/ohpc/pub/compiler/gcc/9.3.0 module load
*openmpi 4.0.4 /opt/ohpc/pub/mpi/openmpi4-gnu9 module load openmpi4
AFNI /opt/ohpc/pub/apps/afni module load afni
Freesurfer 7.2.0 /opt/ohpc/pub/apps/freesurfer/7.2.0 module load freesurfer/7.2.0
PyQt4 4.12.3 /opt/ohpc/pub/libs/gnu9/PyQt4/4.12.3 module load py3-PyQt4/4.12.3